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  <title>GenBank to FASTA</title>
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  <div class="category">
    Format Conversion
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  <div class="program">
    <a href="combine_fasta.html" onmouseover="self.status='Combines multiple FASTA entries into a single sequence.'; return true;" onmouseout="self.status=' '; return true;">-Combine FASTA</a><br />
    <a href="embl_fasta.html" onmouseover="self.status='Returns the entire sequence contained in an EMBL file in FASTA format.'; return true;" onmouseout="self.status=' '; return true;">-EMBL to FASTA</a><br />
    <a href="embl_feat.html" onmouseover="self.status='Parses the feature table of an EMBL file and returns the feature sequences.'; return true;" onmouseout="self.status=' '; return true;">-EMBL Feature Extractor</a><br />
    <a href="embl_trans.html" onmouseover="self.status='Parses the feature table of an EMBL file and returns the protein translations.'; return true;" onmouseout="self.status=' '; return true;">-EMBL Trans Extractor</a><br />
    <a href="filter_dna.html" onmouseover="self.status='Removes non-DNA characters from text.'; return true;" onmouseout="self.status=' '; return true;">-Filter DNA</a><br />
    <a href="filter_protein.html" onmouseover="self.status='Removes non-protein characters from text.'; return true;" onmouseout="self.status=' '; return true;">-Filter Protein</a><br />
    <a href="genbank_fasta.html" onmouseover="self.status='Returns the entire sequence contained in a GenBank file in FASTA format.'; return true;" onmouseout="self.status=' '; return true;">-GenBank to FASTA</a><br />
    <a href="genbank_feat.html" onmouseover="self.status='Parses the feature table of a GenBank file and returns the feature sequences.'; return true;" onmouseout="self.status=' '; return true;">-GenBank Feature Extractor</a><br />
    <a href="genbank_trans.html" onmouseover="self.status='Parses the feature table of a GenBank file and returns the protein translations.'; return true;" onmouseout="self.status=' '; return true;">-GenBank Trans Extractor</a><br />
    <a href="one_to_three.html" onmouseover="self.status='Converts single letter amino acid codes to three letter codes.'; return true;" onmouseout="self.status=' '; return true;">-One to Three</a><br />
    <a href="range_extract_dna.html" onmouseover="self.status='Reads a list of positions and ranges and returns those parts of a DNA sequence.'; return true;" onmouseout="self.status=' '; return true;">-Range Extractor DNA</a><br />
    <a href="range_extract_protein.html" onmouseover="self.status='Reads a list of positions and ranges and returns those parts of a protein sequence.'; return true;" onmouseout="self.status=' '; return true;">-Range Extractor Protein</a><br />
    <a href="rev_comp.html" onmouseover="self.status='Determines the reverse-complement, reverse, or complement of the sequence you enter.'; return true;" onmouseout="self.status=' '; return true;">-Reverse Complement</a><br />
    <a href="split_codons.html" onmouseover="self.status='Separates bases according to codon position.'; return true;" onmouseout="self.status=' '; return true;">-Split Codons</a><br />
    <a href="split_fasta.html" onmouseover="self.status='Converts a FASTA sequence into multiple sequences.'; return true;" onmouseout="self.status=' '; return true;">-Split FASTA</a><br />
    <a href="three_to_one.html" onmouseover="self.status='Converts three letter amino acid codes to one letter codes.'; return true;" onmouseout="self.status=' '; return true;">-Three to One</a><br />
    <a href="window_extract_dna.html" onmouseover="self.status='Returns DNA sequence segments specified by a position and window size.'; return true;" onmouseout="self.status=' '; return true;">-Window Extractor DNA</a><br />
    <a href="window_extract_protein.html" onmouseover="self.status='Returns protein sequence segments specified by a position and window size.'; return true;" onmouseout="self.status=' '; return true;">-Window Extractor Protein</a><br />
    <a href="to_base_32.html" onmouseover="self.status='Returns a nucleotide sequence in base 32 system'; return true;" onmouseout="self.status=' '; return true;"><b>Convert to base-32</b></a><br />
    <a href="to_iupac_codes.html" onmouseover="self.status='Returns a nucleotide sequence in iupac code system'; return true;" onmouseout="self.status=' '; return true;"><b>Convert to IUPAC</b></a>
  </div>

  <div class="category">
    Sequence Analysis
  </div>

  <div class="program">
    <a href="codon_plot.html" onmouseover="self.status='Plots codon frequency (according to the codon table you enter) for each codon in a DNA sequence.'; return true;" onmouseout="self.status=' '; return true;">-Codon Plot</a><br />
    <a href="codon_usage.html" onmouseover="self.status='Returns a standard codon usage table.'; return true;" onmouseout="self.status=' '; return true;">-Codon Usage</a><br />
    <a href="cpg_islands.html" onmouseover="self.status='Returns a list of potential CpG islands.'; return true;" onmouseout="self.status=' '; return true;">-CpG Islands</a><br />
    <a href="dna_mw.html" onmouseover="self.status='Calculates the molecular weight of DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-DNA Molecular Weight</a><br />
    <a href="dna_pattern.html" onmouseover="self.status='Returns positions of the patterns you enter.'; return true;" onmouseout="self.status=' '; return true;">-DNA Pattern Find</a><br />
    <a href="dna_stats.html" onmouseover="self.status='Returns basic sequence statistics.'; return true;" onmouseout="self.status=' '; return true;">-DNA Stats</a><br />
    <a href="fuzzy_search_dna.html" onmouseover="self.status='Returns sequences that are identical or similar to a query sequence.'; return true;" onmouseout="self.status=' '; return true;">-Fuzzy Search DNA</a><br />
    <a href="fuzzy_search_protein.html" onmouseover="self.status='Returns sequences that are identical or similar to a query sequence.'; return true;" onmouseout="self.status=' '; return true;">-Fuzzy Search Protein</a><br />
    <a href="ident_sim.html" onmouseover="self.status='Accepts aligned sequences in FASTA format and calculates the identity and similarity of each sequence pair.'; return true;" onmouseout="self.status=' '; return true;">-Ident and Sim</a><br />
    <a href="multi_rev_trans.html" onmouseover="self.status='Can be used to predict a DNA sequence in another species using a protein sequence alignment.'; return true;" onmouseout="self.status=' '; return true;">-Multi Rev Trans</a><br />
    <a href="mutate_for_digest.html" onmouseover="self.status='Finds DNA sequences that can easily be converted to a restriction site.'; return true;" onmouseout="self.status=' '; return true;">-Mutate for Digest</a><br />
    <a href="orf_find.html" onmouseover="self.status='Determines the positions of open reading frames.'; return true;" onmouseout="self.status=' '; return true;">-ORF Finder</a><br />
    <a href="pairwise_align_codons.html" onmouseover="self.status='Returns the optimal global alignment for two coding DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align Codons</a><br />
    <a href="pairwise_align_dna.html" onmouseover="self.status='Returns the optimal global alignment for two DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align DNA</a><br />
    <a href="pairwise_align_protein.html" onmouseover="self.status='Returns the optimal global alignment for two protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Pairwise Align Protein</a><br />
    <a href="pcr_primer_stats.html" onmouseover="self.status='Returns a report describing PCR primer properties'; return true;" onmouseout="self.status=' '; return true;">-PCR Primer Stats</a><br />
    <a href="pcr_products.html" onmouseover="self.status='Generates PCR products from a template and two primer sequences.'; return true;" onmouseout="self.status=' '; return true;">-PCR Products</a><br />
    <a href="protein_gravy.html" onmouseover="self.status='Returns the grand average of hydropathy value of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein GRAVY</a><br />
    <a href="protein_iep.html" onmouseover="self.status='Returns the predicted isoelectric point of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein Isoelectric Point</a><br />
    <a href="protein_mw.html" onmouseover="self.status='Calculates the molecular weight of protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Protein Molecular Weight</a><br />
    <a href="protein_pattern.html" onmouseover="self.status='Returns positions of the patterns you enter.'; return true;" onmouseout="self.status=' '; return true;">-Protein Pattern Find</a><br />
    <a href="protein_stats.html" onmouseover="self.status='Returns basic sequence statistics.'; return true;" onmouseout="self.status=' '; return true;">-Protein Stats</a><br />
    <a href="rest_digest.html" onmouseover="self.status='Converts the sequence you enter into restriction fragments.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Digest</a><br />
    <a href="rest_summary.html" onmouseover="self.status='Returns the number and positions of restriction sites.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Summary</a><br />
    <a href="rev_trans.html" onmouseover="self.status='Can be used to convert protein into DNA.'; return true;" onmouseout="self.status=' '; return true;">-Reverse Translate</a><br />
    <a href="translate.html" onmouseover="self.status='Returns the translation in the reading frame you specify.'; return true;" onmouseout="self.status=' '; return true;">-Translate</a>
  </div>

  <div class="category">
    Sequence Figures
  </div>

  <div class="program">
    <a href="color_align_cons.html" onmouseover="self.status='Colors a sequence alignment based on sequence conservation.'; return true;" onmouseout="self.status=' '; return true;">-Color Align Conservation</a><br />
    <a href="color_align_prop.html" onmouseover="self.status='Colors a protein alignment based on biochemical properties of residues.'; return true;" onmouseout="self.status=' '; return true;">-Color Align Properties</a><br />
    <a href="group_dna.html" onmouseover="self.status='Numbers and groups DNA according to your specifications.'; return true;" onmouseout="self.status=' '; return true;">-Group DNA</a><br />
    <a href="group_protein.html" onmouseover="self.status='Numbers and groups amino acids according to your specifications.'; return true;" onmouseout="self.status=' '; return true;">-Group Protein</a><br />
    <a href="primer_map.html" onmouseover="self.status='Shows PCR primer annealing sites, translations, and restriction sites.'; return true;" onmouseout="self.status=' '; return true;">-Primer Map</a><br />
    <a href="rest_map.html" onmouseover="self.status='Shows restriction sites and protein translations.'; return true;" onmouseout="self.status=' '; return true;">-Restriction Map</a><br />
    <a href="trans_map.html" onmouseover="self.status='Shows protein translations.'; return true;" onmouseout="self.status=' '; return true;">-Translation Map</a>
  </div>

  <div class="category">
    Random Sequences
  </div>

  <div class="program">
    <a href="mutate_dna.html" onmouseover="self.status='Introduces random mutations into DNA sequences.'; return true;" onmouseout="self.status=' '; return true;">-Mutate DNA</a><br />
    <a href="mutate_protein.html" onmouseover="self.status='Introduces random mutations into protein sequences.'; return true;" onmouseout="self.status=' '; return true;">-Mutate Protein</a><br />
    <a href="random_coding_dna.html" onmouseover="self.status='Generates a random coding sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random Coding DNA</a><br />
    <a href="random_dna.html" onmouseover="self.status='Generates a random DNA sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random DNA Sequence</a><br />
    <a href="random_dna_regions.html" onmouseover="self.status='Replaces regions of the DNA sequences you enter with random bases.'; return true;" onmouseout="self.status=' '; return true;">-Random DNA Regions</a><br />
    <a href="random_protein.html" onmouseover="self.status='Generates a random protein sequence of the length you specify.'; return true;" onmouseout="self.status=' '; return true;">-Random Protein Sequence</a><br />
    <a href="random_protein_regions.html" onmouseover="self.status='Replaces regions of the protein sequences you enter with random residues.'; return true;" onmouseout="self.status=' '; return true;">-Random Protein Regions</a><br />
    <a href="sample_dna.html" onmouseover="self.status='Samples bases from a DNA sequence with replacement.'; return true;" onmouseout="self.status=' '; return true;">-Sample DNA</a><br />
    <a href="sample_protein.html" onmouseover="self.status='Samples residues from a protein sequence with replacement.'; return true;" onmouseout="self.status=' '; return true;">-Sample Protein</a><br />
    <a href="shuffle_dna.html" onmouseover="self.status='Randomly shuffles the DNA sequences you enter.'; return true;" onmouseout="self.status=' '; return true;">-Shuffle DNA</a><br />
    <a href="shuffle_protein.html" onmouseover="self.status='Randomly shuffles the protein sequences you enter.'; return true;" onmouseout="self.status=' '; return true;">-Shuffle Protein</a>
  </div>

  <div class="category">
    Miscellaneous
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  <div class="program">
    <a href="iupac.html" onmouseover="self.status='IUPAC codes for DNA and protein.'; return true;" onmouseout="self.status=' '; return true;">-IUPAC codes</a><br />
    <a href="genetic_code.html" onmouseover="self.status='The genetic codes used in the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Genetic codes</a><br />
    <a href="browser_compat.html" onmouseover="self.status='Browser compatibility.'; return true;" onmouseout="self.status=' '; return true;">-Browser compatibility</a><br />
    <a href="mirror.html" onmouseover="self.status='Mirror the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Mirror this site</a><br />
    <a href="mirror.html" onmouseover="self.status='Use the Sequence Manipulation Suite off-line.'; return true;" onmouseout="self.status=' '; return true;">-Use this site off-line</a><br />
    <a href="about.html" onmouseover="self.status='About the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-About this site</a><br />
    <a href="acknowledgments.html" onmouseover="self.status='Acknowledgments.'; return true;" onmouseout="self.status=' '; return true;">-Acknowledgments</a><br />
    <a href="reference.html" onmouseover="self.status='Citing the Sequence Manipulation Suite.'; return true;" onmouseout="self.status=' '; return true;">-Reference</a>
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            The Sequence Manipulation Suite Copyright &copy; 2000, 2004 Paul Stothard. Send questions and comments to stothard@ualberta.ca
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                <td class="sms">Sequence Manipulation Suite:</td>
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                <td class="title">GenBank to FASTA</td>
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                <td class="description">
                  GenBank to FASTA accepts a GenBank file as input and returns the entire DNA sequence in FASTA format. Use this program when you wish to quickly remove all of the non-DNA sequence information from a GenBank file.<br />
                  <br />

                  <form action="" name="main_form" id="main_form">
                    Paste the contents of one or more GenBank files into the text area below. Input limit is 200000 characters.<br />
                    <textarea rows="6" cols="81">
LOCUS       SUSFASCIN    2320 bp    mRNA            INV       14-MAR-2000
DEFINITION  Strongylocentrotus purpuratus fascin (FSCN1) mRNA, complete cds.
ACCESSION   L12047
VERSION     L12047.1  GI:161470
KEYWORDS    actin bundling protein; fascin.
SOURCE      Strongylocentrotus purpuratus.
  ORGANISM  Strongylocentrotus purpuratus
            Eukaryota; Metazoa; Echinodermata; Echinozoa; Echinoidea;
            Euechinoidea; Echinacea; Echinoida; Strongylocentrotidae;
            Strongylocentrotus.
REFERENCE   1  (bases 1 to 2320)
  AUTHORS   Kane,R.E.
  TITLE     Actin polymerization and interaction with other proteins in
            temperature-induced gelation of sea urchin egg extracts
  JOURNAL   J. Cell Biol. 71 (3), 704-714 (1976)
  MEDLINE   77051438
REFERENCE   2  (bases 1 to 2320)
  AUTHORS   Bryan,J. and Kane,R.E.
  TITLE     Separation and interaction of the major components of sea urchin
            actin gel
  JOURNAL   J. Mol. Biol. 125 (2), 207-224 (1978)
  MEDLINE   79091184
REFERENCE   3  (bases 1 to 2320)
  AUTHORS   Bryan,J., Edwards,R., Matsudaira,P., Otto,J. and Wulfkuhle,J.
  TITLE     Fascin, an echinoid actin-bundling protein, is a homolog of the
            Drosophila singed gene product
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 90 (19), 9115-9119 (1993)
  MEDLINE   94022326
FEATURES             Location/Qualifiers
     source          1..2320
                     /organism="Strongylocentrotus purpuratus"
                     /db_xref="taxon:7668"
                     /dev_stage="larva"
     gene            1..2320
                     /gene="FSCN1"
     CDS             85..1575
                     /gene="FSCN1"
                     /function="actin bundling protein"
                     /note="putative"
                     /codon_start=1
                     /product="fascin"
                     /protein_id="AAC37183.1"
                     /db_xref="GI:161471"
                     /translation="MPAMNLKYKFGLVNSAGRYLTAEKFGGKVNASGATLKARQVWIL
                     EQEESSTISYLKAPSGNFLSADKNGNVYCSVEDRTEDADTGFEIELQPDGKWALKNVS
                     HQRYLACNGEELICSESSTSNPSANWTVQLAIHPQVCMKNVQHQRYAHLKTSEEGEDS
                     VVVDELVPWGADSTLTLVYLGKGKYGLEAFNGKFVQTDGQLAGTANEQTQFTLIFTSG
                     HLVLRDNNGRHLGVDSGTRVLKSSKPGLTKANYFILEDSCPQGAFEFGGKYASLKQGE
                     DVSFKLLVDEDIEDTETFQLEFVETDKYAIRVCDPKKNSRDAKFWKTVAAGIQANGNS
                     KDQTDCQFSVEYNGNDMHVRAPGGKYVSVRDNGHLFLQDSPKDFIFRLLNRPKLVLKC
                     PHGFVGMKEGKAEVACNRSNFDVFTVTYKEGGYTIQDSCGKYWSCDDSSRIVLGEAAG
                     TFFFEFHELSKFAIRAESNGMLIKGEQSGLFTANGSEVSKDTLWEF"
     polyA_signal    2155..2160
                     /gene="FSCN1"
BASE COUNT      699 a    510 c    528 g    583 t
ORIGIN      
        1 acttgaaagt ggataaaatc gactgatacc aaaacaacat tgttttacag aagtggtcgt
       61 ttgaggacat caacatattt cacaatgcct gctatgaatt taaaatacaa atttggcctg
      121 gtcaactcgg ccggcagata cctcactgct gagaagtttg gtggcaaagt caatgcctca
      181 ggagcaacgt taaaagccag gcaagtatgg atcctagagc aagaagagag cagcacgatc
      241 agctacttga aggcgccctc tggtaacttc ctctctgcag ataaaaacgg taacgtctat
      301 tgcagtgttg aggacaggac ggaggacgcg gatacaggat tcgagatcga gttgcaaccc
      361 gatggtaaat gggccctcaa gaatgtttct caccagaggt acctagcttg caatggtgag
      421 gagctgatct gcagtgaatc cagcaccagc aacccctcag caaactggac tgtccagctg
      481 gccatccatc cacaggtctg catgaagaac gtccagcacc aacgctacgc acatctcaaa
      541 accagtgagg agggtgaaga cagcgtggtt gtagacgaat tggttccctg gggagctgat
      601 tccacactca ctcttgtcta cctgggcaaa ggaaagtacg gccttgaggc cttcaacgga
      661 aagtttgtcc aaaccgacgg acagcttgct ggcacagcca acgaacagac gcagttcaca
      721 ctcatcttca catccggtca cctggtacta agggacaaca atggacgtca cttaggagtg
      781 gacagtggaa ccagggtctt gaagtcctcc aagcctggac tgacgaaagc caattacttc
      841 atcctagagg atagctgtcc acaaggtgcc ttcgaatttg gtggcaaata tgcatcgtta
      901 aagcaaggcg aagatgtttc attcaagctt cttgttgacg aagatatcga agacacagag
      961 accttccagt tggagttcgt tgaaaccgac aagtatgcca tcagggtatg tgaccccaag
     1021 aagaactcca gagatgctaa gttctggaag accgtcgctg ctggtatcca ggctaacggc
     1081 aactcaaagg accagacgga ctgtcaattc tctgtcgaat acaacggcaa cgacatgcat
     1141 gtgcgtgctc caggaggcaa gtatgttagt gtccgtgaca acggccatct cttccttcag
     1201 gattcaccca aagacttcat cttccgtctg ctcaaccgac ccaagctggt gctcaagtgc
     1261 cctcatggat tcgtgggcat gaaggagggc aaggctgagg tcgcctgcaa ccgatcaaac
     1321 tttgatgtct tcactgtcac ctacaaggaa ggcggataca ctatccaaga ctcctgtggc
     1381 aagtactggt cttgtgatga cagtagccgc atcgttcttg gagaggcagc aggtactttc
     1441 ttcttcgagt tccatgagct ctccaagttt gctatccgag cagaaagcaa cggcatgttg
     1501 atcaagggcg agcagagtgg cttgtttacc gccaatggtt ccgaggtctc aaaggacaca
     1561 ctgtgggaat tctaaacaaa ttgggcttga aagaagccaa atccaaatca gaagtagagt
     1621 agctgacaag ccagccactc tatctattat atcaattgca aatattgtac atttttttaa
     1681 tacaaaaata ttttcaaagg tgcataataa ttatttcata ctctggtggg atctttagga
     1741 tcatattttc tcattgcctt ggcatactga cttccattat ccctcatttt ttaaaaggta
     1801 aattgatcac ttaatatcaa ctgaaaacga aatggaagta ggtctctgga aatttagaag
     1861 aatagatgac tatccagtat attcaaatat ttgttgaacc tgtctcaaaa aaaccccata
     1921 aaaaaccctc tgttttgtgc tgtctcatag ccataaatag agatcaattc tggtggtata
     1981 tgctacttaa aatcaggctt gaaatagaat aaatggaatg gaatggattt tcaaaaagat
     2041 ttggaatttt aaatttgcag ccagtgtccg tgacaactct tgcataccag aagcactaaa
     2101 cagtctctgc cgcaccgctc gcccaggtgt attgttgtga ctgtactttt gaacaataaa
     2161 acagatcttt tcgtcaagtt tggatataaa agtggattga aatgcacgaa tagattcgac
     2221 ttgtataggg catggtggac attgatttta cagatacttt caatataccg gtaaaaatca
     2281 atcatataga aaatgaaaac agggtgtaat atctcaaata 
//
</textarea><br />

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                      Please check the <a href="browser_compat.html">browser compatibility</a> page before using this program.
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                  *You can <a href="mirror.html">mirror this page</a> or <a href="mirror.html">use it off-line</a>.<br />
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                    <a href="genbank_fasta.html" target="_blank">new window</a> | <a href="index.html">home</a> | <a href="reference.html">citation</a>
                  </center><span class="version">Mon Jan 11 18:25:34 2010</span>
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